Abstract
The development of ‘molecular-omic’ tools and computing analysis platforms have greatly enhanced our ability to assess the impacts of agricultural practices and crop management protocols on soil microbial diversity. However, biotic factors are rarely factored into agricultural management models. Today it is possible to identify specific microbiomes and define biotic components that contribute to soil quality. We assessed the bacterial diversity of soils in 51 potato production plots. We describe a strategy for identifying a potato-crop-productivity bacterial species balance index based on amplicon sequence variants. We observed a significant impact of soil texture balances on potato yields; however, the Shannon and Chao1 richness indices and Pielou’s evenness index poorly correlated with these yields. Nonetheless, we were able to estimate the portion of the total bacterial microbiome related to potato yield using an integrated species balances index derived from the elements of the bacterial microbiome that positively or negatively correlate with residual potato yields. This innovative strategy based on a microbiome selection procedure greatly enhances our ability to interpret the impact of agricultural practices and cropping system management choices on microbial diversity and potato yield. This strategy provides an additional tool that will aid growers and the broader agricultural sector in their decision-making processes concerning the soil quality and crop productivity.
Highlights
Soil microbial communities are impacted by meteorology [1,2], soil properties [3,4,5], agricultural management practices [6,7,8,9] and cropping systems [10,11]
The 51 samples of the 13 fields described in Table 1 were distributed between sand to loam textures (Sand: 30; Loamy sand: 8; Sandy loam to Loam: 13) and 4 classes of potato (Red round:18; White round: 20; Russet: 11; Yellow:3)
After the application of the DADA2 pipeline, the average sequence rate per sample was 18613 for a total of 949242 sequences for the 51 samples. 2008 different amplicon sequence variant (ASV) were observed in the dataset
Summary
Soil microbial communities are impacted by meteorology [1,2], soil properties [3,4,5], agricultural management practices [6,7,8,9] and cropping systems [10,11]. The diverse composition of archaea, bacteria, fungi, protista and other eukaryotic communities found in soil and in the rhizosphere impacts the quality of soil, water and air resources [12], the degradability of organic matter [13] as well as the uptake of nutrients by plants [14,15]. Specific soil microbial groups can suppress soil-borne plant pathogens [16].
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